VMD plugin to calculate and visualize clusters of conformations for a trajectory
☆24Oct 24, 2018Updated 7 years ago
Alternatives and similar repositories for clustering
Users that are interested in clustering are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Convenience functions for VMD-TCL scripting☆14Apr 3, 2026Updated 3 months ago
- ☆11Oct 18, 2019Updated 6 years ago
- Fast PBC wrapping and unwrapping for VMD☆27Nov 25, 2024Updated last year
- ☆39Dec 6, 2012Updated 13 years ago
- Building and analyzing residue interaction networks with cofactors (includes tutorial).☆19Mar 31, 2021Updated 5 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Instructions for Building Software on Various Platforms☆17May 12, 2025Updated last year
- Development version of the pbctools plugin for VMD.☆17Aug 19, 2025Updated 11 months ago
- Workshop - Analysis of Molecular Dynamics Simulation Using Python☆20Aug 14, 2020Updated 5 years ago
- PARCE version 1.0☆12Feb 1, 2021Updated 5 years ago
- ☆13Dec 29, 2022Updated 3 years ago
- A Python package to compute and analyze transport properties.☆17Jul 27, 2025Updated 11 months ago
- Utilities for working with the RDKit☆20Sep 5, 2016Updated 9 years ago
- Using supervised machine learning to build collective variables for accelerated sampling☆28Jun 26, 2018Updated 8 years ago
- Official repo of the Biomeccanica Multiscala course (prof. Marco A. Deriu) - Master Degree in Biomedical engineering, Politecnico di Tori…☆12Jan 2, 2025Updated last year
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- An efficient approach to RMSD-Based HDBSCAN Clustering of long Molecular Dynamics☆18Sep 11, 2022Updated 3 years ago
- Learning Protein-Ligand Properties with Atomic Environment Vectors☆10Apr 19, 2024Updated 2 years ago
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆35Dec 10, 2025Updated 7 months ago
- Implements the blood brain barrier score described in: J. Med. Chem. 2019, 62, 21, 9824-9836 (https://doi.org/10.1021/acs.jmedchem.9b0122…☆14Sep 27, 2020Updated 5 years ago
- Source code for "Nucleosome plasticity is a critical element of chromatin liquid–liquid phase separation and multivalent nucleosome inter…☆13Jun 17, 2022Updated 4 years ago
- Collection of scripts that integrates docking, virtual screening, similarity and molecular modeling programs.☆32Jul 13, 2026Updated last week
- De novo drug design with deep interactome learning☆42Mar 20, 2026Updated 4 months ago
- iPBSA minimizes docked receptor-ligand conformations in implicit solvent and calculates the binding free energy with MM/PB(GB)SA methods.…☆13Oct 10, 2023Updated 2 years ago
- Official repository for the Deep Docking protocol☆130Nov 30, 2023Updated 2 years ago
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- WaterDock-2.0 implementation with Akshay Sridhar☆21Nov 2, 2023Updated 2 years ago
- example demonstrating a free energy estimation starting from OFF and OpenMM☆12Oct 21, 2020Updated 5 years ago
- ☆56Nov 24, 2022Updated 3 years ago
- ☆19Sep 14, 2022Updated 3 years ago
- A Python package to calculate, visualize and analyze correlation maps of proteins.☆43Updated this week
- Small molecules discovery with different active deep learning strategies. Codebase for the paper: "Traversing chemical space with active …☆28Aug 18, 2024Updated last year
- COSMO: COarse-grained Simulation of intrinsically disordered prOteins with openMM☆15Jul 14, 2026Updated last week
- ☆15Dec 4, 2023Updated 2 years ago
- MD pharmacophores and virtual screening☆34Dec 15, 2023Updated 2 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Generate customized voxel representations of protein-ligand complexes using GPU.☆11Sep 8, 2025Updated 10 months ago
- Robust and stable clustering of molecular dynamics simulation trajectories.☆20Sep 2, 2022Updated 3 years ago
- Enumerate conformational, protomeric, and pH-related microstates for docking with AutoDock☆56Updated this week
- A novel approach to pose selection in protein-ligand docking based on graph theory.☆20Nov 22, 2016Updated 9 years ago
- ☆38Jan 8, 2021Updated 5 years ago
- Personalized Network-based Anti-Cancer Therapy Appointment☆11Dec 22, 2025Updated 7 months ago
- A software research tool for the analysis of structural communication in protein ensembles☆14Mar 24, 2022Updated 4 years ago